PA3343 / HsbD (Q9HYQ2) review notes

Summary of the literature

PA3343 (HsbD) is a 389-aa protein with six predicted TM helices (UniProt Phobius,
52-204; MASE8 domain, Pfam PF20968) and a C-terminal GGDEF domain (252-389). My scan
of the UniProt sequence finds the GGEEF motif at 302 and an RxxD I-site (RPLD) at
293.

Literature search (Europe PMC, 2026-11-05, mostly 503 errors; PubMed web search
"HsbD aeruginosa" returned PMID:27792789). Primary data:

  1. Kulasekara et al. 2006 PMID:16477007; full text read on PMC (PMC1413825).
  2. Table 1: "PA3343 GGEEF +(22) PA3702 GGEEF +(445) PA3825 EVL +(27)" (pmol
    c-di-GMP per mg wet cell weight in extracts of overexpressing PA14; detection
    limit 12).
  3. "pellicle formation (hyperbiofilm) was observed for insertions in PA0861 ,
    PA3311 , PA3343 , PA4332 , PA4367 , and PA5017".
  4. "P. aeruginosa expressing PA2870 and PA3343, two DGCs that produce high levels
    of c-di-GMP in our assay ( Table 1 ), do not cause an alteration in the biofilm
    phenotype."
  5. Valentini et al. 2016 PMID:27792789, full text cached. Named HsbD; links it to
    the HptB-HsbR-HsbA pathway. Congo-red staining of E. coli expressing HsbD, lost
    with a GGAAF active-site mutant; I-site c-di-GMP binding by DRaCALA. In a ΔhptB
    background hsbD deletion lowers c-di-GMP and abolishes the hyperbiofilm phenotype
    (complemented), and the ΔhptBΔhsbD mutant hyper-swarms about 9-fold. ΔhsbD is
    deficient in chemotaxis and twitching. HsbD-YFP localises to the cell periphery
    with polar foci. Note: the paper states that PA3343 made 445 pmol/mg in
    Kulasekara's assay PMID:27792789; Table 1 of PMID:16477007 gives 22 for PA3343 and 445 for the
    next row, PA3702 (WspR). The citation misreads the table by one row; it does not
    affect the conclusion that PA3343 is active.
  6. Eilers et al. 2022 PMID:35935233: ΔhsbD slightly increased attachment
    PMID:35935233.

The direction of HsbD's effect on biofilm differs by background: positive in ΔhptB
(PMID:27792789), negative or neutral in single mutants (PMID:16477007,
PMID:35935233).

PseudoCAP IBA-seed assessment

PTN node node term n_seeds leaf IBAs seed annotation (term, evidence, PMID) verdict rationale other seeds IBD stands without this seed?
PTN002895344 GO:0052621 diguanylate cyclase activity 19 205 (28 taxa) GO:0052621, IDA, PMID:16477007 (PseudoCAP) SOUND Extracts of the overexpressing strain contained 22 pmol c-di-GMP/mg, above the 12 pmol detection limit (full text read). Valentini 2016 confirms activity with a GGAAF control in E. coli (full text read). E. coli DosC, DgcC/J/M/N/P/Q/Z; B. subtilis DgcK, DgcP; Shewanella DgcS; P. aeruginosa WspR, SadC, GcbA, DgcP, PA3177, PA1107, PA2870 Yes; see PA1107 notes. No GO_CENTRAL defect for the MF.

PTN002895351 (GO:0043709 IBD): the node-level GO_CENTRAL defect is recorded once in
PA1107-ai-review.yaml (see PA1107 notes); not repeated here.

Annotation decisions